Hands-on Ex3 : Processing Visualising Flow Data

Author

Flora Phyo Zin Htet

Overview

In this hands-on exercise, learn how to build an OD matrix.

Getting Started

The code chunk below install and load sf and tidyverse packages into R environment.

pacman::p_load(tmap, sf, DT, stplanr,
               performance,
               ggpubr, tidyverse)

Preparing the Flow Data

Importing the OD data

Firstly, we will import the Passenger Volume by Origin Destination Bus Stops data set downloaded from LTA DataMall by using read_csv() of readr package.

odbus <- read_csv("data/aspatial/origin_destination_bus_202310.csv")
Rows: 5694297 Columns: 7
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (5): YEAR_MONTH, DAY_TYPE, PT_TYPE, ORIGIN_PT_CODE, DESTINATION_PT_CODE
dbl (2): TIME_PER_HOUR, TOTAL_TRIPS

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Let use display the odbus tibble data table by using the code chunk below.

glimpse(odbus)
Rows: 5,694,297
Columns: 7
$ YEAR_MONTH          <chr> "2023-10", "2023-10", "2023-10", "2023-10", "2023-…
$ DAY_TYPE            <chr> "WEEKENDS/HOLIDAY", "WEEKDAY", "WEEKENDS/HOLIDAY",…
$ TIME_PER_HOUR       <dbl> 16, 16, 14, 14, 17, 17, 17, 7, 14, 14, 10, 20, 20,…
$ PT_TYPE             <chr> "BUS", "BUS", "BUS", "BUS", "BUS", "BUS", "BUS", "…
$ ORIGIN_PT_CODE      <chr> "04168", "04168", "80119", "80119", "44069", "2028…
$ DESTINATION_PT_CODE <chr> "10051", "10051", "90079", "90079", "17229", "2014…
$ TOTAL_TRIPS         <dbl> 3, 5, 3, 5, 4, 1, 24, 2, 1, 7, 3, 2, 5, 1, 1, 1, 1…

A quick check of odbus tibble data frame shows that the values in OROGIN_PT_CODE and DESTINATON_PT_CODE are in numeric data type. Hence, the code chunk below is used to convert these data values into character data type.

odbus$ORIGIN_PT_CODE <- as.factor(odbus$ORIGIN_PT_CODE)
odbus$DESTINATION_PT_CODE <- as.factor(odbus$DESTINATION_PT_CODE) 

Extracting the study data

For the purpose of this exercise, we will extract commuting flows on weekday and between 6 and 9 o’clock.

odbus6_9 <- odbus %>%
  filter(DAY_TYPE == "WEEKDAY") %>%
  filter(TIME_PER_HOUR >= 6 &
           TIME_PER_HOUR <= 9) %>%
  group_by(ORIGIN_PT_CODE,
           DESTINATION_PT_CODE) %>%
  summarise(TRIPS = sum(TOTAL_TRIPS))
`summarise()` has grouped output by 'ORIGIN_PT_CODE'. You can override using
the `.groups` argument.
datatable(odbus6_9)
Warning in instance$preRenderHook(instance): It seems your data is too big for
client-side DataTables. You may consider server-side processing:
https://rstudio.github.io/DT/server.html

We will save the output in rds format for future used

write_rds(odbus6_9, "data/rds/odbus6_9.rds")

The code chunk below will be used to import the save odbus6_9.rds into R environment.

odbus6_9 <- read_rds("data/rds/odbus6_9.rds")

Working with Geospatial Data

For the purpose of this exercise, two geospatial data will be used. They are:

  • BusStop: This data provides the location of bus stop as at last quarter of 2022.

  • MPSZ-2019: This data provides the sub-zone boundary of URA Master Plan 2019.

Both data sets are in ESRI shapefile format.

Importing geospatial data

Two geospatial data will be used in this exercise, they are:

busstop <- st_read(dsn = "data/geospatial",
                   layer = "BusStop") %>%
  st_transform(crs = 3414)
Reading layer `BusStop' from data source 
  `D:\zhphyo\ISSS624\Hands-on_Ex3\data\geospatial' using driver `ESRI Shapefile'
Simple feature collection with 5161 features and 3 fields
Geometry type: POINT
Dimension:     XY
Bounding box:  xmin: 3970.122 ymin: 26482.1 xmax: 48284.56 ymax: 52983.82
Projected CRS: SVY21
mpsz <- st_read(dsn = "data/geospatial",
                   layer = "MPSZ-2019") %>%
  st_transform(crs = 3414)
Reading layer `MPSZ-2019' from data source 
  `D:\zhphyo\ISSS624\Hands-on_Ex3\data\geospatial' using driver `ESRI Shapefile'
Simple feature collection with 332 features and 6 fields
Geometry type: MULTIPOLYGON
Dimension:     XY
Bounding box:  xmin: 103.6057 ymin: 1.158699 xmax: 104.0885 ymax: 1.470775
Geodetic CRS:  WGS 84
mpsz
Simple feature collection with 332 features and 6 fields
Geometry type: MULTIPOLYGON
Dimension:     XY
Bounding box:  xmin: 2667.538 ymin: 15748.72 xmax: 56396.44 ymax: 50256.33
Projected CRS: SVY21 / Singapore TM
First 10 features:
                 SUBZONE_N SUBZONE_C       PLN_AREA_N PLN_AREA_C       REGION_N
1              MARINA EAST    MESZ01      MARINA EAST         ME CENTRAL REGION
2         INSTITUTION HILL    RVSZ05     RIVER VALLEY         RV CENTRAL REGION
3           ROBERTSON QUAY    SRSZ01  SINGAPORE RIVER         SR CENTRAL REGION
4  JURONG ISLAND AND BUKOM    WISZ01  WESTERN ISLANDS         WI    WEST REGION
5             FORT CANNING    MUSZ02           MUSEUM         MU CENTRAL REGION
6         MARINA EAST (MP)    MPSZ05    MARINE PARADE         MP CENTRAL REGION
7                   SUDONG    WISZ03  WESTERN ISLANDS         WI    WEST REGION
8                  SEMAKAU    WISZ02  WESTERN ISLANDS         WI    WEST REGION
9           SOUTHERN GROUP    SISZ02 SOUTHERN ISLANDS         SI CENTRAL REGION
10                 SENTOSA    SISZ01 SOUTHERN ISLANDS         SI CENTRAL REGION
   REGION_C                       geometry
1        CR MULTIPOLYGON (((33222.98 29...
2        CR MULTIPOLYGON (((28481.45 30...
3        CR MULTIPOLYGON (((28087.34 30...
4        WR MULTIPOLYGON (((14557.7 304...
5        CR MULTIPOLYGON (((29542.53 31...
6        CR MULTIPOLYGON (((35279.55 30...
7        WR MULTIPOLYGON (((15772.59 21...
8        WR MULTIPOLYGON (((19843.41 21...
9        CR MULTIPOLYGON (((30870.53 22...
10       CR MULTIPOLYGON (((26879.04 26...
mpsz <- write_rds(mpsz, "data/rds/mpsz.rds")

Geospatial data wrangling

Combining Busstop and mpsz

Code chunk below populates the planning subzone code (i.e. SUBZONE_C) of mpsz sf data frame into busstop sf data frame.

busstop_mpsz <- st_intersection(busstop, mpsz) %>%
  select(BUS_STOP_N, SUBZONE_C) %>%
  st_drop_geometry()
Warning: attribute variables are assumed to be spatially constant throughout
all geometries
datatable(busstop_mpsz)

Before moving to the next step, it is wise to save the output into rds format.

write_rds(busstop_mpsz, "data/rds/busstop_mpsz.rds")  

Next, we are going to append the planning subzone code from busstop_mpsz data frame onto odbus6_9 data frame.

od_data <- left_join(odbus6_9 , busstop_mpsz,
            by = c("ORIGIN_PT_CODE" = "BUS_STOP_N")) %>%
  rename(ORIGIN_BS = ORIGIN_PT_CODE,
         ORIGIN_SZ = SUBZONE_C,
         DESTIN_BS = DESTINATION_PT_CODE)
Warning in left_join(odbus6_9, busstop_mpsz, by = c(ORIGIN_PT_CODE = "BUS_STOP_N")): Detected an unexpected many-to-many relationship between `x` and `y`.
ℹ Row 25632 of `x` matches multiple rows in `y`.
ℹ Row 673 of `y` matches multiple rows in `x`.
ℹ If a many-to-many relationship is expected, set `relationship =
  "many-to-many"` to silence this warning.

Before continue, it is a good practice for us to check for duplicating records.

duplicate <- od_data %>%
  group_by_all() %>%
  filter(n()>1) %>%
  ungroup()

If duplicated records are found, the code chunk below will be used to retain the unique records.

od_data <- unique(od_data)

It will be a good practice to confirm if the duplicating records issue has been addressed fully.

Next, we will update od_data data frame cwith the planning subzone codes.

od_data <- left_join(od_data , busstop_mpsz,
            by = c("DESTIN_BS" = "BUS_STOP_N")) 
Warning in left_join(od_data, busstop_mpsz, by = c(DESTIN_BS = "BUS_STOP_N")): Detected an unexpected many-to-many relationship between `x` and `y`.
ℹ Row 167 of `x` matches multiple rows in `y`.
ℹ Row 672 of `y` matches multiple rows in `x`.
ℹ If a many-to-many relationship is expected, set `relationship =
  "many-to-many"` to silence this warning.
duplicate <- od_data %>%
  group_by_all() %>%
  filter(n()>1) %>%
  ungroup()
od_data <- unique(od_data)
od_data <- od_data %>%
  rename(DESTIN_SZ = SUBZONE_C) %>%
  drop_na() %>%
  group_by(ORIGIN_SZ, DESTIN_SZ) %>%
  summarise(MORNING_PEAK = sum(TRIPS))
`summarise()` has grouped output by 'ORIGIN_SZ'. You can override using the
`.groups` argument.

It is time to save the output into an rds file format.

write_rds(od_data, "data/rds/od_data.rds")
od_data <- read_rds("data/rds/od_data.rds")

Visualising Spatial Interaction

In this section, you will learn how to prepare a desire line by using stplanr package.

Removing intra-zonal flows

We will not plot the intra-zonal flows. The code chunk below will be used to remove intra-zonal flows.

od_data1 <- od_data[od_data$ORIGIN_SZ!=od_data$DESTIN_SZ,]

Creating desire lines

In this code chunk below, od2line() of stplanr package is used to create the desire lines.

flowLine <- od2line(flow = od_data1, 
                    zones = mpsz,
                    zone_code = "SUBZONE_C")
Creating centroids representing desire line start and end points.

Visualising the desire lines

To visualise the resulting desire lines, the code chunk below is used.

tmap_options(check.and.fix = TRUE) 

tm_shape(mpsz) +
  tm_polygons() +
flowLine %>%  
tm_shape() +
  tm_lines(lwd = "MORNING_PEAK",
           style = "quantile",
           scale = c(0.1, 1, 3, 5, 7, 10),
           n = 6,
           alpha = 0.3)
Warning: The shape mpsz is invalid. See sf::st_is_valid
Warning in g$scale * (w_legend/maxW): longer object length is not a multiple of
shorter object length
Warning in g$scale * (x/maxW): longer object length is not a multiple of
shorter object length

When the flow data are very messy and highly skewed like the one shown above, it is wiser to focus on selected flows, for example flow greater than or equal to 5000 as shown below.

tmap_options(check.and.fix = TRUE) 
tm_shape(mpsz) +
  tm_polygons() +
flowLine %>%  
  filter(MORNING_PEAK >= 5000) %>%
tm_shape() +
  tm_lines(lwd = "MORNING_PEAK",
           style = "quantile",
           scale = c(0.1, 1, 3, 5, 7, 10),
           n = 6,
           alpha = 0.3)
Warning: The shape mpsz is invalid. See sf::st_is_valid
Warning in g$scale * (w_legend/maxW): longer object length is not a multiple of
shorter object length
Warning in g$scale * (x/maxW): longer object length is not a multiple of
shorter object length